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chaining with DP

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Heng Li
2017-05-09 22:20:57 +08:00
parent 2827c29b48
commit 949d9be872
2 changed files with 65 additions and 9 deletions
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index.c
+6 -4
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@@ -60,7 +60,7 @@ const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
void mm_idx_stat(const mm_idx_t *mi)
{
int i, n = 0;
int i, n = 0, n1 = 0;
uint64_t sum = 0, len = 0;
for (i = 0; i < mi->n_seq; ++i)
len += mi->seq[i].len;
@@ -71,11 +71,13 @@ void mm_idx_stat(const mm_idx_t *mi)
khint_t k;
if (h == 0) continue;
for (k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k))
if (kh_exist(h, k)) {
sum += kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
if (kh_key(h, k)&1) ++n1;
}
}
fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d; average occurrences: %.3lf; average spacing: %.3lf\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, (double)sum / n, (double)len / sum);
fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum);
}
uint32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)